Mass Effect: The Human-Covenant War
by Shepard2189
Summary: Commander Shepard uncovered the Reaper threat during the last few years of the Human-Covenant War. After Shepard killed Saren and stopped the Collectors, he is recruited by Admiral Hackett to be part of a special mission for the UNSC. This mission is the start of humanity's war with the Reapers, and the final months of the war with the Covenant. Covers ME3, and Halo: CE to Halo 3
1. Chapter 1

**August 7, 2552**

Admiral Hackett and Admiral Anderson stood in Admiral Hood's office. Admiral Hood just told the two of them about OPERATION: RED FLAG.

"We have the personnel we want to include. As I have said, Captain Keyes will be the commanding officer of the Pillar of Autumn. Do you have any questions or comments?" Admiral Hood asked

Admiral Hackett said, "There is the question of Commander John Shepard. He had led a similar operation when he worked for Cerberus. He was tasked with the destruction of the Collector homeworld. He used the Omega-4 Relay to go to the galactic core, and he wiped out the base. There were no reported casualties in his squad"

"That is impressive. I'm surprised he isn't a Spartan himself. I'm hesitant to have him lead the mission though. He is still a Council Spectre, and I would rather not get the Council angry with us. Violence hasn't broken out between the Council and the Covenant, and the UNSC could lose the Council's support if they learn a Spectre led an attack on the Covenant"

"He is acting on behalf of the UNSC" Admiral Anderson pointed out, "Wouldn't that make a difference?"

"We could have him in a supportive role" Admiral Hackett suggested, "Do we have any possible Spectre candidates in our ranks?"

Admiral Hood pulled up a list of UNSC and Alliance personnel that are considered for Spectres. The Master Chief was in the top five, but everyone in the UNSC is very hesitant to give the Chief over to the Council. Not to anyone's surprise, the Council is also hesitant to have a supersoldier be one of their Spectre agents. Lieutenant Commander Ashley Williams showed up right below his name though.

"We can add Commander Williams to the roster as Captain Keyes' XO. Commander Shepard can be on the mission as an evaluator for her Spectre status" Admiral Hood suggested

"We can tell the Council that Operation: Red Flag was not the Commander's idea, and that he was unknowingly dragged into it" Hackett said, "The Council may be suspicious, but they never look too closely"

"Why Commander Williams though? She and Shepard are in a relationship. It wouldn't be professional if Shepard was also her evaluator" Anderson pointed out

"She is also the only friend of Shepard's that we can contact, and she is also the only friend who will not raise suspicions. We can ask the turian or the quarian, but I will not risk an incident on board the Pillar of Autumn" Hackett said, "The last thing we want is for there to be an injured, or worse, dead turian or quarian"

"She is also the only friend of Shepard's who also worked alongside the Spartans" Anderson added, after a moment's thought. Anderson said, "If I recall correctly, Shepard and Williams served with Spartans 117, 104, 058, 087, and 005?"

"That is correct" Hood replied, "That is exactly why I believe Commander Williams should accompany Commander Shepard. Both of them worked with the Spartans, and they are familiar with each other. The official cover story is that Commander Shepard is observing Commander Williams as a potential Spectre candidate"

"That works" Hackett said, and he asked Admiral Anderson, "Is that good for you too?" Admiral Anderson said yes, and Admiral Hackett said, "Good. I will notify Commander Shepard first, and then I will notify Commander Williams"

Admiral Hackett saluted the two admirals, and he left his office. Various UNSC personnel saluted on him his way to his office. He trusted Shepard to be able to handle this. Shepard had made good decisions, like killing the Rachni Queen and saving the Council during Sovereign's attack, and Shepard is able to make even a krogan stand in line. Shepard standing up to Urdnot Wrex is probably one of the more awe inspiring stories about the legendary Commander.

Admiral Hackett walked into his office, and he sat down in front of his terminal. He directed his AI to send a call to the Normandy SR2. Fortunately, the Commander picked up a short time after that.

"Commander Shepard, this is Admiral Hackett, UNSC HQ" Admiral Hackett said, "I will keep this brief. There is a top secret operation being planned for our war with the Covenant. I cannot give you the full details, not unless you tell me if you will work with us. What I can tell you is that it involves the Spartans you served with, and one of your old crew"

Shepard noticeably sat straighter, and he said, "I'm in. What are the details?"

Admiral Hackett appreciated Shepard's willingness to sign up for a mission. Hackett said, "The mission is called Operation: Red Flag. The objective is to capture a Covenant ship and bring it to the Covenant home world. When we get there, we want to retrieve a Prophet and use him as a bargaining chip in negotiations for peace. Considering the mission you had just went on, I imagine this will not be too different"

"Can I use the Normandy? Or any of my crew?"

"The Normandy is a nice ship, but I'm afraid that it is still too weak to go up against a Covenant ship. Chances are, the mission will involve going up against an entire fleet. Against those odds…."

Shepard frowned, and he said, "The Normandy would be obliterated against those odds. What about the crew? They aren't UNSC personnel, but they all got the job done"

"They did, but like you said, they are not UNSC personnel. This mission requires strict military discipline, and to be honest, some of your squadmates may be too unstable for this task. The aliens on board are an incident waiting to happen on a UNSC ship. Not all humans understand that the Council and non Covenant races are not enemies. To some, every race that isn't human is an enemy of the UNSC. I'm sorry, you can't bring your friends with you"

"I understand. You said one of my old friends is joining?"

"Yes. Lieutenant Commander Ashley Williams. She has served us well during your time with Cerberus. She has climbed through the ranks. After our conversation, I will notify her of her placement as the XO of the Pillar of Autumn's crew"

Shepard's eyes widened, and he asked, "Sir, are you asking me to helm the Pillar of Autumn?"

"No, you will be there to assist the mission. Captain Keyes will be the commanding officer of the Pillar of Autumn. If a Spectre led the mission, the UNSC could receive penalties from the Council for attacking the Covenant. If the Council was already at war, you can bet I would have made you the captain of the Pillar of Autumn"

"What will happen to the Normandy while I'm gone?"

"The Normandy will be repaired and upgraded. I hate to admit it, but it is only a matter of time before the Covenant finds Earth. We need to be prepared"

"What about the Reapers, sir?"

"There is a chance the Reapers may be involved. The Spartans who served with you had found a Reaper artifact on Sigma Octanus IV. They discovered that the Forerunner relic on the planet wasn't the only thing the Covenant was after. The Covenant were after a Reaper artifact as well, and that artifact has recently become active"

"Active? Do you think it could be responding to an incoming invasion fleet?"

"It is possible. It is also possible that the entire population was indoctrinated by the artifact. That could explain why it was never reported, and why the colony got a reputation for being full of strange people"

Shepard shuddered, and he asked, "Is the Reaper artifact destroyed?"

"Fortunately, yes. Once the Spartans realized what it was, they destroyed the artifact. ONI was upset, but I would rather not have our intelligence agency become indoctrinated. The impending Reaper invasion makes Operation Red: Flag even more urgent. We can't afford to be divided when the Reapers invade"

"Understood. I will bring the Normandy to Earth as soon as I say goodbye to my crew. I do have one request, sir"

"Go ahead, Commander"

"I know that Cerberus is an enemy faction, but my squad and my crew are good people. They have not committed any atrocities while they served on board. Their service files are also clean. Can you grant them all a pardon?"

Admiral Hackett paused for a moment to look over the files. He sighed, and he said, "I'm sorry, but they were still with Cerberus. However, because they hadn't tried to attack any UNSC assets, they will only be imprisoned. As for your pilot, Flight Lieutenant Moreau, and Dr. Chakwas, they can walk free. The same goes for your squadmates"

"Sir?" Shepard asked, surprised to hear the admiral's decision.

"We understand that Cerberus had come to Lieutenant Moreau and Dr. Chakwas with a claim that they had your body, and they were reviving you. We also understand that they had attempted to contact other members of your squad and the Spartans. For various reasons, the rest of your squad and the Spartans refused Cerberus' offer to join them. It is likely none of them believed Cerberus was bringing you back. We have reason to believe Cerberus was attempting to manipulate your squad"

Shepard frowned, and he said, "Lieutenant Commander Williams told me that when we met on Horizon. She told me that she didn't believe Cerberus had my body. When they offered to protect her family, she suspected that Cerberus was threatening them. She killed the agents, and she moved her family off-world"

"I see. I believe they promised Lieutenant Moreau that they can keep Tiptree, the colony his family lives on, safe, and they promised your doctor a chance to help bring you back to life"

"I imagine Joker was already willing to try trusting Cerberus. He saw me die, and Cerberus used his survivor's guilt against him"

"They did. That is why Lieutenant Moreau and Dr. Chakwas are free to walk. They were coerced to work with Cerberus, as I imagine you were. Your reports indicate that the Illusive Man effectively cut you off from the Council and the UNSC by publicly announcing your allegiance with Cerberus. On that note, you are also free from all charges. You are not a traitor, and turning your back against the only people looking after the Reapers at the time would have been irresponsible. You made the right decision. As for your squadmates, they were following your orders, not Cerberus'. Bring the Normandy to Earth ASAP. From there, you will be put on a quick trip to Reach, where the Pillar of Autumn is waiting. As I said, the Normandy will be undergoing repairs. EDI, your ship's AI, will also be checked for signs of rampancy"

"Understood, sir. I want to advise you that I have a geth in my squad. He's friendly"

"Thank you for telling us. We will make sure it gets off Cairo Station without incident. Dismissed"

Shepard disconnected from the call, and he ordered, "Joker, tell the squad to assemble in the briefing room"

"Roger that" Joker said

Shepard stood up from his terminal, and he walked to leave his cabin. EDI, the Normandy's AI, said, "We will be fine, Shepard"

"Are you sure? You told me about what Cerberus had done to you while I was gone"

EDI paused for a second, which for an AI was the equivalent of a five minute pause. EDI said, "I have checked my systems, and Reaper augmentation did not appear to push me into rampancy, at least not permanently. However, it is possible that I became a metastable AI"

"Wait, EDI is metastable?" Joker asked, "That can't be right! Can it?"

"Or maybe I am rampant, after all"

Shepard took a step back, and Joker coughed over the intercom. EDI said, "That was a joke"

"Not funny, EDI" Shepard said sternly

"I can assure you, all of my functions and systems are intact. Aside from the upgrades Cerberus made, I am the same as I was on the first Normandy"

"I'm glad to hear it"

Shepard stepped into the elevator, and he took it down to the second deck. His reunion with EDI was probably one of the more traumatic parts of being brought back to life. On the first Normandy, EDI was a standard smart AI. She was created specifically for the Normandy. In some ways, it was almost as if the Normandy was her actual body. When the first Normandy was destroyed, Cerberus had recovered both his body and EDI. One Cerberus cell was in charge of reviving Shepard, and another was in charge of understanding how the Reapers had managed to avoid rampancy. Shepard still remembered Miranda telling him that the Illusive Man had come close to shutting down EDI permanently a few times.

The elevator doors opened, and Shepard walked out of the elevator. He walked into the briefing room, where his whole squad waited for him. They all had concerned looks on their faces, or at least most of them did. Grunt looked like he was ready for another mission. Shepard felt a pang of sadness, but he knew he had to let his crew go.

"I have gathered you all here with sad news" Shepard said, without preamble, "I was contacted by Admiral Hood of the UNSC. He has asked me to be part of an important mission. He has also ordered me to hand over the Normandy to the UNSC"

"Those fuckers?" Jack spat, "You can't do that! They will arrest me on sight!"

"They are likely going to execute me and Miranda" Jacob pointed out, "We worked for Cerberus"

"I asked Admiral Hackett to be easy on you guys. You all served me well, and you don't deserve to be executed"

"Damn right we don't!" Jack said

"We are going to Earth, where the Normandy will be put into dry dock and upgraded. None of you can join me on this mission"

"None of us?" Garrus asked, "You sure?"

"Are you sure we can't help you? We helped out in the Collector's Base" Tali said

"That's different. I will be part of a UNSC led mission, and that is all I can say. I was told that this mission is to only have UNSC personnel"

"Damn" Zaeed said, "The UNSC must be really scared about something to want to keep aliens off. Normally, they welcome any help from non Covenant races"

"I agree. This is unusual" Samara observed, "But I trust you Shepard. I trust that this mission will not violate the Code"

"It won't" Shepard said, but he didn't truly believe it. Admiral Hackett talked about invading an enemy empire's homeworld. Can he really pull a gun on an alien child? Even if that alien is part of the enemy species? The image of him shooting a Sangheili child chilled him.

"You are all free to go when we get to Earth. Joker, what's the ETA to Earth?"

"ETA is one hour, sir"

Shepard looked at his squad. Everyone was silent, and they looked at each other. Jack was the first one to speak up. She banged the table, and she said, "Man! Fuck those UNSC bastards! Just when we thought we were free of trouble, it comes back to us! I am going to miss you, Shepard. It was great, and we had a lot of fun. Just….don't die, Shepard. Or I will kill you myself!"

"Noted, and I will miss you too, Jack" Shepard said, "I won't die"

"Don't make promises you can't keep" Jack said with a small smile, and she said to Miranda, "Hear that, precious? It will be just you and me on a personal shuttle once we leave Earth"

Miranda glared at her, and she said, "I will miss you too, Shepard. It has been an honor, and I appreciate you helping me out with my sister. You…have done more for me than Cerberus ever has for me. Cerberus gave me money, a career, and resources. You gave me a chance to save my sister, and I thank you for that"

"And I thank you for helping me with my father. I also thank you for saving my hide more than once" Jacob said, "It has been a privilege. Maybe drinks on the Citadel when you are back?"

"That sounds good, Jacob, and you are paying this time" Shepard said

"You are going to owe me some kills when you get back" Grunt said, "We still have plenty to kill, and you better come back with good stories"

Mordin glanced at Grunt, and he said, "Interesting priorities. Sheaprd leaving. Not concerned about Shepard's possible death, only concerned about his kill count." Mordin turned his attention to Shepard and said, "Will miss you, Shepard. Don't know much about the mission, but I can guess. Glad you picked me to help. Happy to help. Someone else would have gotten it wrong"

"It was great working with you too, Mordin" Shepard said

"Yes. I found our time together…to be a good way to spend one's life, as mine comes to a close. I am glad to have made some amends before I die. You helped me out with Kolyat, and I am grateful for that" Thane said

"I am also grateful for your help with my daughter. She was the reason why I became a Justicar, and she is why I have followed this life for centuries. She was my sole mission in life for so long, that I do not know what my mission will be. For now, I will do as you do. I will right wrongs in the galaxy, and I will strive to make the galaxy a better place. I am honored to have fought alongside you, and I hope we meet again" Samara said

Zaeed and Kasumi looked at each other. Kasumi gently nudged Zaeed, and she said, "You do it first"

Zaeed grunted, and he said, "Well Shepard, it has been one hell of a ride. We went in, blew up those Collector bastards, and kicked the Shadow Broker in the face. Well, the former one. I won't kick Liara in the face, even if she annoys me. It has been a goddamn good ride, even with Vido escaping"

"It has been fun Shepard" Kasumi said, "Infiltrating Hock's estate, fighting a hornet, and saving the galaxy from the Collectors. See you around the galaxy, Shep! And thanks, for letting me keep the greybox"

"Shepard-Commander, we have an inquiry" Legion said, "We have calculated your chances of survival on this mission to be really low. Yet you seem to believe that you will come back. Why is that?"

"Because we have beaten the odds before" Shepard said, "They said I couldn't find Ilos. I found it. They said the Collector Base was a suicide mission. We all survived. I bet I will survive this too, and I will see you all on the other side"

"We wish you luck, Shepard-Commander"

Shepard looked at Garrus and Tali. So far, neither one had spoken. Garrus was the first one of the two to speak.

"Shepard, I honestly can't believe I am not joining you this time. We fought against Saren and the Collectors, and now I need to sit aside while the UNSC sends you off on a suicide mission of their own. Well, I honestly can't blame them. They can't have a turian sniper stealing their kills" Garrus said

"Yeah. That would make the UNSC marine corps, the ODSTs, and the Spartans look lazy" Shepard joked

"Well, I wouldn't say all the Spartans, but yes, most of them would look lazy" Garrus said, "Tell that Spartan sniper to know that the only reason why she is able to get kills is because I am not there to steal them. Thank you again for helping me with Sidonis. Sparing him was the right choice"

"I am glad you see that, and I will tell the Spartan what you said about her sniping, Garrus. See you on the other side"

"Shepard, I am still surprised I can't join you, but I can understand the reasons. I'm a quarian, and not everyone trusts us, even after I helped you beat Saren. I will do what I can to make sure the quarian Flotilla is ready for the Reapers. Thank you again for helping me with my trial. I just received a message from the Fleet, it looks like I will be an admiral! It isn't official yet, they wanted to tell me before they announced it to the Fleet. I will be here, waiting for you Shepard. It has been a fun ride going after Saren and the Collectors. I hope we can work together again when you return"

"We will work together again, I promise Tali. You too, Garrus. I can't fight the Reapers without either of you two"

"Good" Garrus said, and he joked, "Someone has to make up for your sniping skills"

"And someone has to make sure you don't drive off the mountains" Tali added

"And I appreciate your help with that, Tali" Shepard said with a light chuckle, and he said to Garrus, "I think we may need to have a sniping match when I get back"

"I will hold you to that, Shepard" Garrus said

Joker said over the intercom, "We are docking at Cairo Station. UNSC personnel will be coming to pick us up shortly"

"Understood. Goodbye guys, it has been an honor serving with you" Shepard said

Everyone in Shepard's squad saluted him. He wasn't surprised to see Miranda and Jacob salute, but he was surprised to see the others do the same. Shepard smiled, and he saluted them back. Shepard turned around, and he left the briefing room. He walked up to the bridge, where Joker was slowly getting out of his seat.

"Well, here we go again" Joker said as he got up, "You are going to leave all of us for some time, and we will go our separate ways"

"Hey, at least I'm not dead this time" Shepard said half jokingly

"Yeah. And you better not die on this suicide mission. EDI filled me in on the conversation you had with Admiral Hackett. This sounds serious. I can't lose you a second time"

"Don't worry Joker, I am coming back" Shepard said

"You better. There is no one else I would rather serve"

"And there is no other pilot I would rather have piloting my ship"

Shepard and Joker saluted each other. The Normandy's hatch opened, and two UNSC marines stepped inside. One of them asked, "Commander Shepard?"

Shepard turned around and said, "That's me. Are you here to take me to my transport?"

"Yes, sir"

The marines turned around, and Shepard started to follow them. EDI said, "Shepard, when you get to Reach….good luck"

"When I'm done with my mission" Shepard started to say

"Don't make a girl a promise…" EDI interrupted him

Shepard turned back towards the marines, and he continued following them. EDI said to Shepard's back, "If you know you can't keep it"


	2. Chapter 2

A/N: I am replacing part of the Fall of Reach with Operation: Red Flag.

Commander Shepard walked away from the Normandy, and he saw Ashley standing by a docking port to a frigate. She was wearing a white UNSC officer's uniform. There were several medals on her left breast. Her long hair was tied up into a regulation bun. Ashley saw him, and she started walking towards him. The two of them hugged each other when Shepard was halfway to the frigate. He was comforted by her warm embrace, as she was by his warm embrace. After everything Shepard had gone through, he was glad to have this break in the grind that was the brutal Human-Covenant War.

"Shepard, you made it back" Ashley said with a smile.

"No thanks to Cerberus, yes. It's good to be back in the UNSC. Where are the Chief and the Spartans?" Shepard asked

"They are on Reach, or at least en route to the colony. I imagine my sisters must be relieved to see so many Spartans coming back. Has Cerberus kept you up to date on the Human-Covenant War?"

Shepard shook his head, and he said, "The Illusive Man kept me in the dark about the UNSC's affairs. For all I know, we had won, and the galaxy has forgotten about me"

Ashley sighed, and she said, "No, we remembered you. Besides, if we forgot you, I am pretty sure those endorsements on the Citadel would help remind them who you are. Is every store on the Citadel your favorite store?"

Shepard chuckled, and he said, "I actually liked all of them. They just wanted endorsements"

"I may have to order the Chief to make an endorsement then, and see what that does" Ashley joked

Shepard paused for a moment, imagining the Spartan saying, "I'm the Master Chief, and this is my favorite store on the Citadel." Shepard said, "That may end up being the only time he will refuse to follow an order"

"Speaking of refusing to follow orders" Ashley said, changing topics, "I heard that you defied the Illusive Man's order to keep the Collector Base, and you told the Illusive Man to go screw himself"

"That's right. I saw what the Collectors were doing to the colonists, and I saw what Cerberus did in Project Overlord. I don't trust Cerberus to not repeat the same mistake"

"Good" Ashley said, "Those Cerberus bastards are the worst. Are Garrus and Tali okay? Did Cerberus hurt them?"

"No, and if they did, the UNSC would be cleaning up the blood of any Cerberus personnel who had hurt them"

"How did Cerberus manage to recruit them?"

"I recruited them, actually. I saved Garrus from a mercenary attack on his base, and I saved Tali from the geth. I don't think I need to tell you their reactions to me blowing up the Collector Base"

"How is Liara? Was Joker telling the truth when he said", Ashley lowered her voice to whisper, "When he said that Liara became the Shadow Broker?"

"Joker was telling the truth. Liara has been doing well since I last saw her. I think we can count on her support in the upcoming Reaper War" Shepard replied

"Good" Ashley said, "Where are Garrus and Tali going now?"

"Tali said she was going back to the Flotilla. She told me that she is going to be an admiral. As for Garrus, he's probably going back to Palaven"

"What about Wrex? I heard he is the leader of the krogan now"

"He is. He actually helped me with Grunt's Rite of Passage. I will explain what that is later"

Shepard and Ashley walked up to the hatch leading to the frigate. The marine at the entrance asked, "Are you Commander Shepard and Commander Williams?"

"That's us" Shepard replied, and the two of them presented their IDs. The marine looked them over, and he said, "Your IDs match your identities. Go on board"

Shepard and Ashley walked to their temporary quarters on the ship. They sat down, and Shepard asked, "Any word on your family? You told me on Horizon that you were relocating them"

"They made it safely to Reach" Ashley said with a smile, "I hope they will be safe there"

"They will be" Shepard said firmly, "It's hard to be a Cerberus agent on Reach and not be identified by someone. My parents are also serving on ships there. My mother is the captain of the UNSC Einstein, a supercarrier co-developed by the UNSC and the asari. It's a gift from the Council, their way of helping us with the war against the Covenant. y father is the captain of the UNSC Savannah"

"A frigate?" Ashley asked, "I thought he was going to be the captain of a much larger vessel"

"He always felt more comfortable being in command of a frigate. He thinks a cruiser is too large for him"

"Frigates also get a lot less attention. Is that why you went to the Bahak System? Was the Normandy the best ship for the job?"

"No, the Normandy had nothing to do with it. Admiral Hackett ordered me to go there because there were reports of a Reaper artifact in the base. He wanted me to confirm the artifact, and destroy it if it proved to be a threat"

"And an entire system got wiped out" Ashley said, remembering the emergency broadcast that showed a blue supernova full of dark energy. Someone had mentioned in the broadcast that such an explosion was only possible if a mass relay exploded.

"That relay was going to be the Reapers' entry point to the galaxy. If I hadn't taken it out, the Reapers would have arrived a few weeks ago. I delayed the invasion by destroying the relay with the asteroid. It was tough, and I had to fight through a base full of indoctrinated soldiers and scientists, but I succeeded"

"Killing 300,000 batarian bastards in the process. If you ask me, there should have been at least a billion batarians on that colony" Ashley said bitterly, "They would have learned how we felt about the Covenant destroying our colonies"

"Agreed"

The batarians were the odd species in the Covenant. They actually did not worship the Forerunners. They had no belief in the Great Journey, and before humanity appeared, they were opposed to the Covenant. When the UNSC was granted an embassy, the batarians were so upset that they joined the Covenant and declared to the galaxy that they worship the Forerunners.

The ship's AI announced, "We are now entering Slipspace. We will arrive at Reach in a few days"

Shepard and Ashley looked at each other. Ashley said, "That's a little faster than usual"

"They must want us at Reach as soon as possible" Shepard said, "This sounds serious"

Ashley suddenly tensed up when she thought of the possibility of the Covenant attacking Reach. Ashley asked, "Do…do you think Reach could be under attack?"

Shepard looked at Ashley, and neither of them said anything. They knew what each other were thinking. A likely reason the UNSC was pushing this mission is that Reach itself was in danger of falling to the Covenant, and they didn't want to lose their chance to turn the war around. Without Reach, all that was left were the several dozen Alliance colonies and Earth itself.

The Systems Alliance is a mere remnant of what it used to be. While the UNSC was struggling with conflicts in the solar system in the 2100s, the Alliance split off from the rest of humanity, and they expanded through the galaxy. It was the Alliance, not the UNSC, who made contact with the turians and the rest of the Council in 2157. It was the Alliance, not the UNSC, who had established some of humanity's first interstellar colonies. The Alliance didn't last long in the galaxy because it wasn't able to sustain itself. Consequently, the Alliance government dissolved, leaving several dozen human colonies that were isolated from the rest of humanity. If the Alliance government hadn't dissolved, the batarians would have joined the Covenant much earlier. When the UNSC started expanding into the galaxy, they rediscovered the isolated colonies and incorporated them into the UNSC. The Alliance colonists still call themselves Alliance though, in honor of humanity's first attempt at interstellar expansion, and they still use Prothean technology rather than the UNSC's technology.

"If Reach is under attack….then we need to get your family out quickly" Shepard said, "I only pray we can get there in time to warn them"

"Me too"

The two of them sat tensely, waiting for the frigate to finish its journey to Reach. When they arrived, they noticed that the planet was already under attack. Shepard and Ashley both stood up, and they walked over to a window. Ashley gasped, and she said, "Oh my God….Reach…." They watched a UNSC vessel pass by them. The ship was firing on a Covenant vessel while it was slowly being destroyed. Ashley thought she saw a Supercarrier in the distance start glassing the surface.

Shepard frowned, and he said, "How could no one know that Reach is under attack? It's one of our biggest colonies!"

"They must have tried to keep it secret….but why?"

The captain of the frigate said, "Commander Shepard, Commander Williams, Captain Keyes of the Pillar of Autumn is contacting us. He requests you board the Pillar of Autumn ASAP"

Shepard and Ashley looked at each other, and Shepard said, "We should go"

Shepard and Ashley made their way through the frigate to the bridge. They saw a massive cruiser floating ahead of them. The words "Pillar of Autumn" were barely visible on the ship's stern. Shepard said into the comm, "This is Commander Shepard. I have Commander Williams with me. I understand you want us to be on the Autumn?"

"Commander, I am relieved you are here. We have little time" Captain Keyes said, "I will brief you as soon as you two are on board. The Spartans are already on board"

"Affirmative"

Shepard and Ashley made their way to the hanger. They passed by numerous marines, who tried to salute them. Shepard passed by some windows, too focused on the impending mission to pay much attention to the battle outside. Fortunately for him, he missed the Savannah's destruction. Ashley managed to catch a glimpse of it though, and she gasped. She whispered, "Shepard….I'm sorry"

Shepard glanced at her, and he asked, "Is something wrong?"

Ashley shook her head, and she said, "I will tell you later. I don't want to distract you right now"

"Commanders, the Pelican is this way!" A marine said

"Thank you" Shepard said, and he went in the direction the marine pointed. Shepard and Ashley climbed into the Pelican, and the hatch closed behind them. The Pelican quickly lifted off, turned around, and sped out of the hanger. In a matter of minutes, the Pelican arrived at the Pillar of Autumn. The Pelican gently entered the hanger bay, turned around, and landed softly. The doors opened, and Shepard and Ashley both saluted Captain Keyes. He was waiting for them in the hanger.

Captain Keyes returned their saltues and said, "At ease. You don't need to salute, Commander Shepard. You are a Spectre after all. You outrank me"

"Not on this ship" Shepard said, "I'm just another officer, or at least that's what Admiral Hackett has told me, sir"

"I see. Come with me"

Captain Keyes turned around and walked towards the bridge with Shepard and Ashley in tow. Keyes asked, "While we are on the way there, tell me what you know so far"

Shepard said, "I know that we have been assigned to the Autumn to assist in a high risk mission, and Commander Williams is your XO, and I'm here as an advisor"

"So not much" Keyes said, "I will tell you the rest, then. You are now part of Operation: Red Flag, which is an attempt to capture the Covenant leadership and return them to the UNSC for negotiations"

Shepard's eyes widened momentarily, and he asked, "Wait, are you saying that we…are going right for their homeworld? Is such a thing possible?"

Keyes glanced at Shepard with an amused smile, and he said, "You are the last person I would expect to say that. But, yes, it is possible. We have seen the battle reports of Spartan Blue Team's deployment in the Battle of the Citadel. They were on a mission to defend the Council, but it was enough to get the top brass thinking about the feasibility of the mission"

"With all due respect sir, I doubt the Covenant has their own Citadel, or that attacking their homeworld is just like attacking the Citadel" Ashley said

"It is…a possibility though, especially since they are an amalgam of species. Palaven, Sur'Kesh, and Thessia are homeworlds of the main Council species, but none of them are the Council's capital. The Citadel is"

The three of them entered the CIC. A screen showing the mission steps was in the middle of the CIC. The ship AI's pedestal flashed, and the ship's AI, Cortana, popped up.

"The Spartans are in position, and they are ready to attack the Covenant Supercarrier" Cortana reported

"Good" Keyes said, "After I brief our last additions to the crew, I will send you with Commander Shepard to the Spartans' Pelicans. He will give you to the Master Chief personally. Do you stand by your decision to be with the Chief? You can change your decision at any time"

"I'm surprised you would ask me that. I have gone over the Spartans' service records. There is no other Spartan I would rather serve with"

"Good. If it was up to me, I would assign you to the Chief myself. Now, Cortana, can you brief these two on Operation: Red Flag?"

Cortana turned to face Shepard and Ashley. Shepard wondered if Cortana's appearance would be…distracting to the crew. The AI wasn't clothed, and although her breasts were barely visible, they were still visible nonetheless. Fortunately, she looked more like a hologram than an actual woman with flesh and bones.

"The first step is to attack and disable a Covenant ship. That is already underway. Long Night of Solace is already under attack, and it is close to being disabled. The second step is to board the ship. That's where you, Commander Shepard, and the Spartans and ODSTs will come in. The third step is to pilot it to High Charity. The fourth step is to capture one of the Covenant's leaders and take him back to force the Covenant into negotiations"

Cortana held a hand up and said, "Hold on a moment. Captain Keyes, I think we are ready to start Phase Two. The Commander should take me to the Chief now"

"I agree" Keyes said, and he waited for Cortana's avatar to disappear. Once the avatar was gone and Cortana's chip was sticking out of the pedestal, Keyes took the chip and handed it to Shepard.

"Get this to the Chief ASAP. I would give you a pistol, but I don't think that would be necessary. The Spartans and ODSTs have already loaded up the Pelicans with the weapons and equipment they will need"

"Yes sir" Shepard said, and he saluted. He walked off the bridge, and started walking towards the Pelicans. A pilot called out, "Sir! We have an incoming transmission from Colonel Holland! He says it's about Noble Team"

Captain Keyes looked up, and he was a little puzzled by the urgent message. Keyes said, "Put it through"

Colonel Holland's face showed up on the view screen. Holland looked tired, and Keyes could hear sounds of people rushing from one place to another. Keyes guessed that one of Holland's operations is not going as planned, or his base is actually close to being attacked by the Covenant. Keyes hoped it was the former.

"Captain Keyes, sir, I noticed you are interested in the Long Night of Solace" Colonel Holland said

"That is correct" Keyes said, and he asked , "Is there something wrong?"

"We have a Spartan on a Corvette headed for a crash course with the Long Night of Solace. The bomb has to be detonated manually….and he has volunteered to detonate it. Please state your intentions with the Supercarrier"

Keyes hesitated, and he said, "I cannot tell you the details as to why I am interested in that ship. However, it is vital that it survives. Do not, I repeat, do not destroy that Supercarrier!"

"Understood. We will relay those orders at once. What do you want me to order the Spartan to do?"

"Tell him to prepare to board the Supercarrier, and to disable the bomb as soon as possible"

"Understood"

Jorge-052 sat by the Pelican, watching the planet rotate below him. The view would be peaceful if it wasn't for the intense space battle around him. He hoped that Noble Six would be able to get back to Noble Team safely. He had a nagging feeling that Reach was still going to fall. He was surprised to hear Colonel Holland contacting him. Jorge-052 put on his helmet and said, "Colonel Holland, sir"

"We have orders for you, Noble Five. You are to not detonate the Slipspace bomb. You are to board the Long Night of Solace as soon as the Corvette docks. Understood?"

"Understood, sir. May I ask why the plan changed?"

"I cannot say. Good luck Noble Five"

Jorge-052 walked over to the makeshift bomb and worked on disabling the bomb. He had a feeling as to why the mission changed, and why the Pillar of Autumn was involved. He vaguely remembered a briefing with Dr. Halsey a few weeks ago with the other Spartan IIs. He suddenly remembered the briefing. It was for Operation: Red Flag! Jorge muttered to himself, "Chief…it has been too long"

On the Pillar of Autumn, Shepard finally made it to the hangers. He saw Blue Team and a large number of other Spartans he didn't recognize. Before he went up to them, he saw Major Silva walk by him. Shepard reached out and stopped him.

"Silva? Antonio Silva, is that you?" Shepard asked, surprised to see a member of his ODST squad on board the Autumn

Unfortunately, Major Silva was not happy to see Shepard. Silva turned around with a scowl on his face.

"Shepard. I see you are not finished betraying the ODSTs you served with" Silva growled

Shepard was offended by both Silva's comment about being a traitor, and Silva not referring to him by rank. "Betrayed? If it's about Cerberus" Shepard started to say, but Silva shut him off.

"Sometimes you are forced into a situation you can't get out of. It happens to everyone. I am referring to your affiliation with them!" Silva jabbed a finger at the Spartans, and he said, "You are buddies with those freaks. Those freaks killed three of our men!"

Shepard crossed his arms, and he said, "As I recall, ODSTs get killed by other ODSTs, or even marines, by accident. Yet we still trust them. They are all human. The same applies to the Spartans"

"One of those freaks tore four ODSTs apart in training!" Silva spat angrily, "This isn't a matter of firing a rocket too close to a warthog, or running someone over in a vehicle!"

"Those…freaks, as you call them, are vital to the UNSC war effort. They also helped me take down Saren, and they stopped the Reapers from invading, at least for now. They are good soldiers, and I could not have asked for better people to serve under my command. Now, unless you want to get kicked off this ship, I suggest you fall in line, follow my orders, and work with the Spartans. Understood?"

Silva saluted, and said, "Sir, yes sir" Silva walked away, but he managed to sneak a glare before he continued walking. Shepard walked over to the armory, and he put on a set of N7 armor. There was a battalion of ODSTs that called themselves "N7", after the Alliance's own version of ODSTs. The armor looked like standard ODST armor, but it had a red stripe on the helmet and a red stripe going down the right arm. Before Shepard put on his armor, he called the Chief over to the armory.

Shepard quickly put on the armor. It wasn't his personal armor though. That was still on the Normandy. The new armor was familiar enough for him to be comfortable with it though. When Shepard put on his helmet, he turned around to see the Chief enter the armory. The Chief saluted, and Shepard returned the salute.

"Commander. It is great to see you back" the Chief said, "We are ready for the mission"

"It's good to be back, Chief. If Major Silva gives you, or any of your Spartans, any trouble, come to me. I will sort him out"

"Understood. You wanted to see me, sir?"

"Captain Keyes wanted me to give you this" Shepard held out Cortana's data chip, "Cortana has chosen to accompany you on the mission"

The Chief took the data chip and inserted it into his helmet. Cortana said, "Huh. Your architecture isn't much different from the Autumn's"

"Don't get any funny ideas" the Chief said

Captain Keyes' voice came over the comm to say, "Boarding parties, the Long Night of Solace is now disabled. You are green to board! I repeat, you are green to board!"

"You heard him" Shepard said, "Move out! All Spartans and ODSTs, board your Pelicans and get ready to board the Long Night of Solace"

"Sir, yes sir!" the Chief said as he saluted, and he walked to his Spartans. The Spartan IIs all got into Pelicans, and they strapped themselves in. The Chief was surprised to see Shepard join them.

"Sir!" The Spartans saluted, and the Chief added, "I'm glad you are with us, sir"

"So am I, Chief" Shepard said, and then he said to all the Spartans and ODSTs in the Pelicans, "Okay, this is the plan. We are going to aim right for the hanger bays in the Long Night of Solace. When we get there, we will make our way to the bridge, and vent out every compartment on the ship into space. On the way there, I want you to divide yourselves into as many teams as you think are necessary. Since there are numerous ways to the bridge, I want you all to take different routes, to cover more ground. Understood?"

"Sir, yes sir" the Spartans and ODSTs all called out

"Good. Now, there is one change to the mission. One more Spartan will be joining us on this mission. One team is to meet up with him and bring him to the bridge. Good luck" Shepard said

The Chief asked, "Sir, permission to be part of your team?"

"Permission granted….and I wasn't going to ask. I was going to order you to be part of my team"

"Sir, permission for Blue Team to join you?" Fred spoke up

"Permission granted. I couldn't do this without you guys. Spartans-029, 059, and 093, you are with us too"

"Understood" Spartans-029, 059, and 093 said

Shepard said, "Spartan-010, you are to lead Red Team. Spartan-006, you are to lead Green Team. Understood?"

"Understood" both Spartans said

Shepard was happy to have Grey Team back. They had come back just in time to rejoin the fight. It was an unexpected discovery, although some suspected that ONI may have had a hand in it. When a UNSC vessel had suffered a Slipspace drive failure near the Rubble, they had stumbled onto Grey Team. Grey Team just happened to have a crippled ship with a working Slipspace drive. The drive was transferred over to the ship with the broken down drive, and the ship was able to bring Grey Team back to UNSC space.

Shepard switched comms, and he asked Major Silva, "Major Silva, what is the status of the ODSTs?"

"We're as ready as we can be" Silva said, "We are ready to kick some Covie ass!"

"Glad to hear it" Shepard said, and then he switched to a private comm channel, and he said to Ashley, "Ash….before I go…."

"Shepard, if you are going to say goodbye….don't bother. You said goodbye when you went on the Suicide Mission, and you came back. You will come back from this. I know you will"

"Thanks, Ash. But in the event I do not come back….finish what I started. Finish the fight against the Reapers and the Covenant"

"Will do, Skipper. If you die, then the first Reaper I kill will be in your name"

Shepard signed off, and he said, "We are ready to go, Captain!"

"Good. All teams, launch!"

The Pillar of Autumn rotated so the hanger bays faced the Long Night of Solace. The bays opened, and several Pelicans shot out of the Autumn and made their way to the Long Night of Solace. If the pilots of the Pelican dropships looked carefully, they would see a small Corvette making its way to the Long Night of Solace. Operation: Red Flag was go.


	3. Chapter 3

**Chapter 3**

Shepard's Pelican managed to slip into one of the Long Night of Solace's hangers. Shepard said, "All teams, once your Pelican lands, you are to immediately disembark, clear out your hanger, and make your way to the bridge."

"Yes sir!" Everyone radioed

Shepard's Pelican opened the doors, and Shepard jumped out. The Chief, Kelly, Fred, and Linda jumped out and formed a tight circle around Shepard. Malcom, Joshua, and Grace formed a triangle around the circle.

"Spread out, but stay together." Shepard said, "I will lead the way"

Shepard walked to the front of the group, and he led his team over to one of the doors. The Spartans all got to either side of the doors. Shepard stood on the left side, and the Chief stood on the right. Kelly knelt down and started a decryption program with her omnitool. When the lock clicked, Kelly sprinted to cover, and she said, "Enemies incoming!"

As if on cue, the doors opened and a large group of Grunts and Jackals were suddenly visible. Several of the Grunts stared at the Spartans in shock before they were gunned down by eight assault rifles. The Grunts and Jackals all spun in the air in the confusion, and in a matter of seconds, there were nothing but bodies littering the hall. The Jackals didn't even have time to raise their shields.

"Hallway secured." the Chief said, "We are ready to move forward."

"Good. Stay tight, and follow me. Blue Four, get in the vents and scout ahead. Snipe any enemies you see."

"Yes sir" Linda responded before she opened a grate. She saw a flicker of an Engineer's tentacle in the vent. She climbed in, took out her pistol, and fired a few rounds at the Engineer. The Engineer squealed, and it fell to the vent's floor.

"Cortana, where did the Corvette dock?" Shepard asked

A waypoint was marked on Shepard's and the Spartans' HUDs. Cortana said, "The Spartan who was riding the Corvette is right outside the Corvette's hatch. Once I get a lock on his armor, I will start tracking him." There was a brief pause, and then Cortana said, "I picked up the Spartan's armor signature. I am tracking him now."

"Good. All teams, head to the bridge! My team will meet with you shortly" Shepard ordered

Cortana asked, "Wouldn't it be better if you had all the teams meet with the Spartan?"

"We need that bridge secured. Besides, if we all focused on meeting the Spartan, the Covenant will have enough time to form defenses around the bridge"

Shepard led his team down several hallways, following Linda's and Cortana's warnings about Covenant movement. They had wanted to get to the Spartan who just joined them as quickly as possible.

Shepard radioed, "Red and Green teams, what are your status?"

"Green team here. We are handling the Covenant without any problems" Jai reported, "We are making our way to the bridge, sir"

"Red Team here. We are experiencing the same thing. The defenses are light" Naomi remarked, and she added, "It's a little…too light, sir"

"I agree. They may be trying to fall back to the bridge. Eliminate as many Covenant as you can find on the way to the bridge"

"Yes sir!" both team leads radioed

Shepard asked, "Cortana, how far are we from the Spartan?"

"You should be in radio contact…..now"

A new voice crackled over the COM. Shepard guessed it was the Spartan they were searching for.

"About time you came on board" Jorge said, "I was wondering when you would show up. I was starting to think I was all by my lonesome up here"

Shepard walked over to the door, and he noticed it was locked. Shepard said, "Blue Two, you know what to do"

Kelly got to the door, but she didn't take out her omnitool. Instead, she gently knocked the door six times. In response, they heard six whistles, and Jorge said, "Good. It's clear on both sides. I'm opening the door now"

The door slid open, and they saw a Spartan holding a mini gun. He was in a room surrounded by many corpses of Grunts, Jackals, and more than a few Elites.

"So…I see you got started without us" the Chief remarked

"You can't get all the kills, Chief" Jorge said, "You gotta let us get some kills too once in a while"

Jorge immediately noticed Shepard's rank on his HUD. Jorge straightened up a little bit, and he said, "Commander, sir! I apologize, I did not notice your rank when you came in"

"It's okay" Shepard said, "To be honest, I am surprised that the UNSC reinstated my rank that quickly. What is your name, Spartan?"

"I'm Warrant Officer Jorge-052, sir. What are my orders?"

"You are to join me and my team of Spartans. We are going to board this ship, and take this to the Covenant's home world to kidnap one of their leaders" Shepard explained

"Understood, sir"

The Chief held his hand up, and he looked towards one of the doors. The Chief pumped his fist twice. Since the Chief and Blue Team served on the first Normandy, Shepard had become familiar with Spartan hand signals.

"Commander, this is Red Team. We just entered the bridge, and there is heavy resistance! Be advised, the Covenant aren't the only enemy on this ship! I repeat, the Covenant aren't the only enemy on this ship!" Naomi radioed

"Understood. Hold the bridge as long as possible. Green Team, assist Red Team ASAP. Be advised, we may up against Reaper forces" Shepard ordered

"Yes sir!" Jai radioed, "We are moving towards the bridge now"

"Blue Four, where are you?" Shepard asked

A waypoint momentarily appeared in Shepard's HUD, and Cortana quickly put a waypoint showing where the bridge was. Shepard noticed that Linda was near the bridge, and he said, "Go to the bridge and provide sniper cover. We will handle ourselves back here" Shepard ordered

A single acknowledgement light winked on in Shepard's HUD. Shepard moved into the large room with the rest of his team. There were three other doors leading to the room they were in. In the center of the room were four low walls forming a square. The Chief asked, "Commander, how do you want us to spread out?"

Shepard said, "Blue Two, Blue Three, and Blue Five, cover the left door. Blue Six, Blue Seven, and Blue Eight, cover the right door. Spartan -052, you are Blue Nine, and you are with me and the Chief. We will cover the center door"

Everyone ran to cover. It was a little crowded in the center, but Shepard would like to not be out in the open. Especially not if there are Reaper forces on board. As if on cue, the doors opened, and Grunts, Jackals, and Elites all spilled into the room. The air was soon full of bullets, plasma bolts, and needler rounds. Shepard noticed that a few of the Grunts, Jackals, and Elites looked very wrong. Shepard popped out of cover and emptied a clip of his assault rifle into an Elite. The Elite roared, and it fell to the ground. The Elite next to it roared, and it charged towards him. Shepard's suspicion that there was something wrong was confirmed when he saw the Elite's arms.

The Elite was definitely a husk. The eyes were glowing orbs, and the arms were both replaced by twisted energy swords. The mandibles were all removed. Dots of blue light covered the Elite's arms and legs. The torso had a large blue circle in the center.

"We have Reaper troops on board! All teams, be advised! We have Reaper forces!" Shepard warned them

"Reaper forces!?" Major Silva yelled, "Shit!"

"Commander, this is Red Team. Green Team just arrived, and we secured the bridge. We lost two Spartans in the fight. We also detected a strange energy signature coming from another part of the ship" Naomi radioed

"Understood. Green Team, stay in the bridge, and make sure no one tries to get on board. Red Team, locate and destroy the Reaper artifact. I don't care how valuable that artifact would be to ONI. The risks are too great for it to be kept intact. Major, I want you to patrol the ship with the ODSTs, search for any survivors."

"Yes sir!"

Several more of the Elite husks poured into the room. Shepard saw a few Grunts and Jackals had been forcibly combined into a grotesque husk. They had the body and legs of a Jackal, and the arms and head of a Grunt.

"There are a ton of these ugly bastards!" Major Silva remarked

"Keep firing!" Shepard ordered

Shepard and Blue Team kept ducking in and out of cover. Shepard would fire while the Chief reloaded, and vice versa. Soon, the entire room was full of Covenant bodies and bodies of husks. Shepard stood up, and he asked, "Did you see many of these things on Reach?"

Jorge nodded grimly, and he said, "I have seen too many of these, sir. Will there be more of them?"

"I think there will be more, especially if there is a Reaper artifact on board this ship"

Kelly spoke up, "There's a chance that every ship in the fleet has a Reaper artifact. If the Covenant's home world is full of those artifacts….."

"Then the mission just got tougher" Shepard said, "That won't matter though. The Reapers had never fought against anything like the Spartans. Major Silva, what is your situation?"

"This is Major Silva. We are under heavy fire, and we need immediate assistance! We were patrolling near the bow of the ship, and we found a large concentration of Covenant and Reaper forces! We need immediate assistance!"

"Sir! This is Red One, requesting immediate back up! We have located the artifact, and the bulk of the Reaper forces on this ship! We are taking heavy losses! We request immediate assistance!" Naomi radioed

"Sir, this is Green One. We need additional reinforcements! The Covenant keep coming, and we are running low on ammo! Reinforcements would be greatly appreciated, sir!" Jai reported

"Sir, with all due respect, I say we should forget about those Spartans! They are nothing but outdated and obsolete fighting machines! You need to save us! You need to save your fellow ODSTs!" Silva barked

Shepard frowned. He didn't like the idea of splitting up his team, but he had no choice. He said, "Blue One, Two, Three, and Five, stay with me. We will go assist Red Team. Blue Six, Seven, Eight, and Nine, you four go to the bridge and assist Green Team"

"What about us, sir!? Are you going to abandon your fellow ODSTs!?" Silva shouted

"Retreat back to the bridge!" Shepard ordered

"You heard him! Move, move, move!" Major Silva yelled.

Shepard cut the link, and he ran towards the artifact with his half of Blue Team. They encountered some Grunts and Jackals along the way, but the Spartans made short work of them. They made their way to a large door where the Reaper artifact was.

"Alert. I am detecting a large concentration of enemy forces on the other side" Cortana warned, "I suggest you reload all your weapons and be prepared for an intense fight"

"Acknowledged" Shepard said, "Blue Two, you know what to do"

Kelly knelt by the door while the other Spartans flanked Shepard. Kelly held out her omnitool, and after a few beeps, the doors unlocked. Shepard radioed, "We are here! How is your team holding up?"

"We have been taking casualties, sir! We are now down to three Spartans, including me. It seems that the Reapers made a bodyguard out of all the Elites!"

As if on cue, a massive Elite ran in front of the artifact. It looked like it was a combination of fifteen Elites and at least a few Brutes smashed together. Fred remarked, "I guess that's where most of the Elites went"

The massive Elite roared at them, and it charged them. Shepard ordered, "Move!" Everyone rolled out of the way, and they ran for cover. Shepard fired a few rounds at the Elite, and then he ducked back into cover. Naomi and Anton ran up to join him behind cover. Shepard looked up in time to see the third Spartan in Green Team get lifted into the air and thrown against a wall. Shepard heard a sickening crack as the Spartan's neck broke.

"I guess this is what has been killing your team?" Shepard asked

"That is correct, sir"

"Do you have any suggestions as to how to kill this thing?"

Cortana said, "I suggest heavy weaponry. There may be a fuel rod cannon nearby. Here, I located one for you"

Shepard saw a nav point show up on his HUD. Shepard said, "All Spartans, keep moving and don't let up! I am going to grab a fuel rod cannon!"

Shepard sprinted away from cover, and he found a fuel rod cannon on the ground. A dead Grunt was on the ground, still holding the cannon firmly in his hands. Shepard yanked the cannon out of the Grunt's hands, and he hefted it over his shoulder. He ran back to cover just in time to see the monster Elite approaching the Chief, Kelly, and Fred.

"Hey! Ugly! Over here!" Shepard yelled

The massive Elite turned around, and Shepard fired a shot from his fuel rod cannon. The Elite roared when the round hit him, and it started making its way towards Shepard. Shepard fired off two more rounds. Both of them slammed into the Elite's arm. The Elite had a hammer for one hand, and an energy sword for the other hand.

The Chief ran up behind the massive Elite and fired a round from a rocket launcher. The rocket slammed into the massive Elite, and it turned around to face him. Shepard and the Chief both fired another round from their respective weapons, and they slammed into the Elite. The Elite roared, and then it fell to the ground.

"Threat neutralized" Shepard said, "Now for the Reaper artifact"

Naomi said, "Sir, we already planted several bombs on the artifact. We were going to blow it up when we were sealed into this room with the Titan"

"Titan?" Shepard asked, "Is that your name for that thing?"

"Yes, sir"

"That's appropriate. Cortana, how far away should we be from the explosion?"

"The bridge is a safe place to be when the explosives go off. I recommend sealing off this room when we leave"

"Agreed. Green Team, we are en route to the bridge. Major Silva, what's your status?"

"This is Lieutenant Vega. Major Silva covered our retreat to the bridge. He locked himself on the other side of a door during our retreat. We heard and felt a massive explosion afterwards…we assume he's KIA."

"Understood. How close are you to the bridge?"

"Shouldn't be too far, Commander."

"Good. We are on our way."

Shepard and his team made their way back to the bridge. Half of the ODSTs that accompanied them were dead. They were now down to 18 Spartan IIs.

"Bridge is secured." Jai reported.

"Good work, Spartans." Shepard said. He looked over at the Chief, and he motioned for him to approach the center console.

The Chief walked over and inserted Cortana into the bridge. Cortana said, "Excellent work. I'm sealing off the bridge, and I'm purging the rest of the ship. I have also found records of the Covenant home world. Or should I say, station. It appears that having a space station be the capital of an empire is not just something the Council does."

"Where is it?" Shepard asked.

"It's…hard to pinpoint. They move High Charity around frequently. You would think the Council would try to do that with the Citadel. That could have come in handy during Sovereign's attack."

"Agreed, but we can tell the Councilors our thoughts about their strategy later. Where's High Charity?"

Cortana opened up the map of the Milky Way, and she zoomed in on a set of coordinates. She said, "They are a few hours of Slipspace travel away from us."

"Good. Jump when you are ready."

Operation Red: Flag Teams  
Blue Team: Master Chief, Kelly, Fred, Linda, James, Malcom-059, Joshua-029, Grace-093, Jorge-052  
Red Team: Naomi-010, Anton-044  
Green Team: Jai-006, Adrianna-111, Mike-120, Will-043, Issac-039, Vinh-030, Li-006  
Deaths in Operation: Red Flag, in order  
Jorge-052  
Malcom-059  
Joshua-029  
Vinh-030  
Issac-039  
Anton-044  
Li-006  
Grace-093  
Installation 04 and First Strike in place of Fall of Reach. Long Night of Solace and Pillar of Autumn meet at a pre designated meet up point. Grey Team transfers to a nearby prowler. Shepard and the others transfers back to the PoA, but the Prophet of Mercy is killed when Thel Vadmee's fleet arrives. The POA jumps to Installation 04. Anton, Li, Grace, and Naomi stay on the Pillar of Autumn while the Chief, Kelly, Fred, Linda, and Will accompany Shepard, Ashley, and James. Anton and Li get converted into the Flood. Grace dies during Operation: First Strike.  
Shepard arrives back on Earth, gets debriefed by the three admirals. Spartan IIs get Mark VI armor. Naomi gets left on Earth to support Admiral Anderson.  
Blue Team: Master Chief, Kelly, Fred, Linda, Will-043  
Intro to ME3 combined with intro of Halo 2  
Eden Prime DLC  
Genophage arc. Kelly gets injured during one of the missions, and Dr. Halsey manages to sneak off the Normandy with her.  
Grunt's mission  
Grissom Academy is attacked by the Covenant. Shepard and crew meets up with Dr. Halsey and Jun, who had escaped in a Cerberus shuttle  
Installation 05 and the splitting of the Covenant in place of the Coup (Basically, one coup switched for another)  
Sangheilios arc  
Rannoch arc  
Ardat Yakshi and Jacob's missions  
Missions with Zaeed, Kasumi, and Thane  
Omega DLC. Shepard and Aria meet up with Grey Team, and they help liberate Omega. Grey Team leaves on another assignment.  
Leviathan DLC  
Shepard and company uncovers secrets concerning the Spartan II program  
Horizon  
Citadel DLC  
Cerberus HQ  
Halo 3 in place of ME:3's Priority Earth. Naomi-010 stays on Earth to help defend it.  
Installation 04B is detonated, the Chief is in the back half of the Forward Unto Dawn, the Arbiter and Shepard are recovered in the front half. The Normandy is transported to Onyx  
Events of Ghosts of Onyx after Fred, Linda, and Will arrive  
Normandy crew is recovered, Ashley and James sign up for the Spartan IV Program  
Ashley and James become part of Sarah Palmer's personal squad


End file.
